TB-Profiler result

Run: SRR25827702
Summary

Run ID: SRR25827702

Sample name:

Date: 16-03-2024 03:07:37

Number of reads: 15434392

Percentage reads mapped: 99.27

Strain: lineage3.1.2;lineage2.2.1

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.His445Leu (0.27), rpoB p.Ser450Leu (0.74)
Isoniazid R fabG1 c.-15C>T (0.73), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Leu (0.23), embB p.Gln497Arg (0.75)
Pyrazinamide R pncA p.Gly132Ala (0.72)
Streptomycin R rpsL p.Lys43Arg (0.75), gid p.Tyr22* (0.27)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.73)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.25
lineage2 East-Asian Beijing RD105 0.75
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.73
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.25
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.25
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.73
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rpoB 761140 p.His445Leu missense_variant 0.27 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.74 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.75 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.73 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.72 pyrazinamide
embB 4247429 p.Met306Leu missense_variant 0.23 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.75 ethambutol
gid 4408137 p.Tyr22* stop_gained 0.27 streptomycin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7581 p.Asp94Arg missense_variant 0.31
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.73
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.73
ccsA 620625 p.Ile245Met missense_variant 0.77
rpoB 759746 c.-61C>T upstream_gene_variant 0.25
rpoC 762434 c.-936T>G upstream_gene_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764840 p.Ile491Val missense_variant 0.73
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.74
mmpR5 779409 c.421_424dupGATC frameshift_variant 0.72
mmpS5 779615 c.-710C>G upstream_gene_variant 0.72
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.77
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.71
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.27
pncA 2289365 c.-125delC upstream_gene_variant 0.24
ahpC 2726105 c.-88G>A upstream_gene_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.73
embC 4241022 p.Ala387Val missense_variant 0.71
embC 4242075 p.Arg738Gln missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.75
embB 4247028 p.Leu172Arg missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 0.76
aftB 4268753 c.84T>G synonymous_variant 0.75
ethA 4327212 p.Thr88Ala missense_variant 0.74
ethA 4327292 p.Thr61Arg missense_variant 0.28
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.73
gid 4407927 p.Glu92Asp missense_variant 0.74